Oceanographic Profiles for Cariaco Chemoautotrophy Paper

Load libraries

library(oce)
library(ocedata)
library(tidyverse)
library(readxl)
library(cowplot)
library(gridGraphics)

Load in and check CTD data. Do some QC of oxygen profiles

CAR212_2 (Leg 2 [Omics cruise] of Cariaco-212)

## C212_2 cast 1

# Load in with oce package
C212_2_1 <- read.oce("CTD_data/C212_2_1.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this name

# Trim the file to only the downcast
C212_2_1_dc <- ctdTrim(C212_2_1)
# Plot full profile
plot(C212_2_1_dc)

# Plot only oxygen
plotProfile(C212_2_1_dc, ytype = "depth", "oxygen5")

# Correct DO by sensor offset
C212_2_1_dc[["oxygen5"]] <- C212_2_1_dc[["oxygen5"]]-0.3 #I had previously determined these offsets by taking the average DO concentration below the chemocline (where conditions are sulfidic and DO is confidently zero). Check "C212_2_ctd_cor.xlsx" for details.
# Plot again
plotProfile(C212_2_1_dc, ytype = "depth", "oxygen5") 

## C212_2 cast 2

# Load in with oce package
C212_2_2 <- read.oce("CTD_data/C212_2_2.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this name

# Trim the file to only the downcast
C212_2_2_dc <- ctdTrim(C212_2_2)
# Plot full profile
plot(C212_2_2_dc)

# Plot only oxygen
plotProfile(C212_2_2_dc, ytype = "depth", "oxygen5")

# Correct DO by sensor offset
C212_2_2_dc[["oxygen5"]] <- C212_2_2_dc[["oxygen5"]]-0.34
# Plot again
plotProfile(C212_2_2_dc, ytype = "depth", "oxygen5") 

## C212_2 cast 3

# Load in with oce package
C212_2_3 <- read.oce("CTD_data/C212_2_3.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this name

# Trim the file to only the downcast
C212_2_3_dc <- ctdTrim(C212_2_3)
# Plot full profile
plot(C212_2_3_dc)

# Plot only oxygen
plotProfile(C212_2_3_dc, ytype = "depth", "oxygen5") 

# Correct DO by sensor offset
C212_2_3_dc[["oxygen5"]] <- C212_2_3_dc[["oxygen5"]]-0.31
# Plot again
plotProfile(C212_2_3_dc, ytype = "depth", "oxygen5") 

## C212_2 cast 4

# Load in with oce package
C212_2_4 <- read.oce("CTD_data/C212_2_4.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this name

# Trim the file to only the downcast
C212_2_4_dc <- ctdTrim(C212_2_4)
# Plot full profile
plot(C212_2_4_dc)

# Plot only oxygen
plotProfile(C212_2_4_dc, ytype = "depth", "oxygen5") 

# Correct DO by sensor offset
C212_2_4_dc[["oxygen5"]] <- C212_2_4_dc[["oxygen5"]]-0.31
# Plot again
plotProfile(C212_2_4_dc, ytype = "depth", "oxygen5") 

# Plot  oxygen data from all casts on same plot
plotProfile(C212_2_1_dc, ytype = "depth", "oxygen5")
lines(C212_2_2_dc[["oxygen5"]], C212_2_2_dc[["depth"]], col = "red")

lines(C212_2_3_dc[["oxygen5"]], C212_2_3_dc[["depth"]], col = "blue")
lines(C212_2_4_dc[["oxygen5"]], C212_2_4_dc[["depth"]], col = "green")

CAR216_2 (Leg 2 [Omics cruise] of Cariaco-216)

## C216_2 cast 1

There were 26 warnings (use warnings() to see them)

# Load in with oce package
C216_2_1 <- read.oce("CTD_data/C216_2_1.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this name

# Trim the file to only the downcast
C216_2_1_dc <- ctdTrim(C216_2_1)
# Plot full profile
plot(C216_2_1_dc)

# Plot only oxygen
plotProfile(C216_2_1_dc, ytype = "depth", "oxygen5")

# Correct DO by sensor offset
C216_2_1_dc[["oxygen5"]] <- C216_2_1_dc[["oxygen5"]]-2.28 #I had previously determined these offsets by taking the average DO concentration below the chemocline (where conditions are sulfidic and DO is confidently zero). Check "C216_2_ctd_cor.xlsx" for details.
# Plot again
plotProfile(C216_2_1_dc, ytype = "depth", "oxygen5") 

## C216_2 cast 2

# Load in with oce package
C216_2_2 <- read.oce("CTD_data/C216_2_2.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this name

# Trim the file to only the downcast
C216_2_2_dc <- ctdTrim(C216_2_2)
# Plot full profile
plot(C216_2_2_dc)

# Plot only oxygen
plotProfile(C216_2_2_dc, ytype = "depth", "oxygen5")

# Correct DO by sensor offset
C216_2_2_dc[["oxygen5"]] <- C216_2_2_dc[["oxygen5"]]-2.3
# Plot again
plotProfile(C216_2_2_dc, ytype = "depth", "oxygen5") 

## C216_2 cast 3

# Load in with oce package
C216_2_3 <- read.oce("CTD_data/C216_2_3.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this name

# Trim the file to only the downcast
C216_2_3_dc <- ctdTrim(C216_2_3)
# Plot full profile
plot(C216_2_3_dc)

# Plot only oxygen
plotProfile(C216_2_3_dc, ytype = "depth", "oxygen5") 

# Correct DO by sensor offset
C216_2_3_dc[["oxygen5"]] <- C216_2_3_dc[["oxygen5"]]-2.29
# Plot again
plotProfile(C216_2_3_dc, ytype = "depth", "oxygen5") 

## C216_2 cast 4

# Load in with oce package
C216_2_4 <- read.oce("CTD_data/C216_2_4.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this name

# Trim the file to only the downcast
C216_2_4_dc <- ctdTrim(C216_2_4)
# Plot full profile
plot(C216_2_4_dc)

# Plot only oxygen
plotProfile(C216_2_4_dc, ytype = "depth", "oxygen5") 

# Correct DO by sensor offset
C216_2_4_dc[["oxygen5"]] <- C216_2_4_dc[["oxygen5"]]-2.29
# Plot again
plotProfile(C216_2_4_dc, ytype = "depth", "oxygen5") 

# Plot  oxygen data from all casts on same plot
plotProfile(C216_2_1_dc, ytype = "depth", "oxygen5")
lines(C216_2_2_dc[["oxygen5"]], C216_2_2_dc[["depth"]], col = "red")

lines(C216_2_3_dc[["oxygen5"]], C216_2_3_dc[["depth"]], col = "blue")
lines(C216_2_4_dc[["oxygen5"]], C216_2_4_dc[["depth"]], col = "green")

CAR224_2 (Leg 2 [SBU cruise] of Cariaco-224)

## C224_2 cast 1

There were 26 warnings (use warnings() to see them)

# Load in with oce package
C224_1 <- read.oce("CTD_data/C224_1.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this namecannot decode longitude or latitude from '** latitude:'cannot decode longitude or latitude from '** longitude:'

# Trim the file to only the downcast
C224_1_dc <- ctdTrim(C224_1)
# Plot full profile
plot(C224_1_dc)

# Plot only oxygen
plotProfile(C224_1_dc, ytype = "depth", "oxygen6")

# Correct DO by sensor offset
C224_1_dc[["oxygen6"]] <- C224_1_dc[["oxygen6"]]-3.53 #I had previously determined these offsets by taking the average DO concentration below the chemocline (where conditions are sulfidic and DO is confidently zero). Check "C224_ctd_cor.xlsx" for details.
# Plot again
plotProfile(C224_1_dc, ytype = "depth", "oxygen6") 

## C224 cast 2

# Load in with oce package
C224_2 <- read.oce("CTD_data/C224_2.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this namecannot decode longitude or latitude from '** latitude:'cannot decode longitude or latitude from '** longitude:'

# Trim the file to only the downcast
C224_2_dc <- ctdTrim(C224_2)
# Plot full profile
plot(C224_2_dc)

# Plot only oxygen
plotProfile(C224_2_dc, ytype = "depth", "oxygen6")

# Correct DO by sensor offset
C224_2_dc[["oxygen6"]] <- C224_2_dc[["oxygen6"]]-3.53
# Plot again
plotProfile(C224_2_dc, ytype = "depth", "oxygen6") 

## C224 cast 3

# Load in with oce package
C224_3 <- read.oce("CTD_data/C224_3.cnv")

unrecognized SBE name 'E'; consider using 'columns' to define this nameunrecognized SBE name 'E10^-8'; consider using 'columns' to define this nameunrecognized SBE name 'N^2'; consider using 'columns' to define this nameunrecognized SBE name 'N'; consider using 'columns' to define this namecannot decode longitude or latitude from '** latitude:'cannot decode longitude or latitude from '** longitude:'

# Trim the file to only the downcast
C224_3_dc <- ctdTrim(C224_3)
# Plot full profile
plot(C224_3_dc)

# Plot only oxygen
plotProfile(C224_3_dc, ytype = "depth", "oxygen6") 

# Correct DO by sensor offset
C224_3_dc[["oxygen6"]] <- C224_3_dc[["oxygen6"]]-3.82
# Plot again
plotProfile(C224_3_dc, ytype = "depth", "oxygen6") 

# Plot  oxygen data from all casts on same plot
plotProfile(C224_3_dc, ytype = "depth", "oxygen6", col = "blue")
lines(C224_1_dc[["oxygen6"]], C224_1_dc[["depth"]], col = "black")

lines(C224_2_dc[["oxygen6"]], C224_2_dc[["depth"]], col = "red")

Next import grab sample data